Summary of Study ST000866

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000575. The data can be accessed directly via it's Project DOI: 10.21228/M8BM2Z This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000866
Study TitleLarge Untargeted Profiling in PAR1 and PAR2 Mice after SCI
Study SummaryLarge Untargeted Profiling in NEFA in PAR1 and PAR2 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21 or 60 mouse spinal cord (SC). There are 30 total sampes, n=5 for each group. wild type control, PAR1 KO and PAR2 KO at P21 and P60 days.
Institute
Mayo Clinic
Last NameScarisbrick
First NameIsobel
Address200 First Street SW, Rochester, MN 55905
Emailscarisbrick.isobel@mayo.edu
Phone507-284-0124
Submit Date2017-08-11
Analysis Type DetailLC-MS
Release Date2021-02-17
Release Version1
Isobel Scarisbrick Isobel Scarisbrick
https://dx.doi.org/10.21228/M8BM2Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000575
Project DOI:doi: 10.21228/M8BM2Z
Project Title:Mayo Pilot and Feasibility: Targeting Myelin Metabolism to Enhance Recovery of Function after SCI
Project Summary:The loss of myelin, degeneration of the myelin producing oligodendroglia and impaired remyelination are essential features of traumatic spinal cord injury (SCI) that significantly limit patient recovery of function. The lipid rich composition of myelin, including exceptionally high levels of saturated fatty acids, underlie its essential physiological roles, including its structural and signaling properties and electrical insulation of axons to facilitate the conduction of nerve impulses. The myelin sheaths also provide metabolic support to the axons they wrap, and myelin health is therefore essential to the maintenance of axon integrity and function in the brain and spinal cord. The primary goal of this Pilot Proposal to the Mayo Clinic Metabolomics Core is to integrate highly sensitive metabolomics liquid chromatography-tandem mass spectrometry (LC/MS/MS) assays to quantify the lipid composition of the myelin membrane, with our conventional neurobehavioral approaches, enabling us to explore the metabolic basis of new interventions capable of promoting myelin regeneration and restoration of patient function. Metabolomics Core expertise in Magnetic Resonance Spectroscopy (NMR) based evaluation of key metabolites involved in CNS injury and repair (N-acetyl-L-aspartate, choline, myo-inositol, glucose/ glutamine and lactate) will also be applied to strengthen our mechanistic understanding of myelin injury and repair. Specifically, utilizing these innovative approaches we will test a novel hypothesis driven by new preliminary findings that the levels of dietary fatty acids can be optimized alone, or in combination with exercise training, to facilitate myelin regeneration and recovery of neurobehavioral function after injury to the adult spinal cord. In Aim 1, we will determine whether alterations in dietary fat, including saturated fat or omega-3 fatty acids, facilitate restoration of the myelin membrane and metabolite signatures of central nervous system repair after experimental SCI in adult mice. In Aim 2, we will determine whether exercise training alone or in combination with dietary fatty acid supplementation fosters myelin regeneration and recovery of function after experimental SCI. The proposed studies will leverage the expertise of the Mayo Metabolomics Core with that of Dr. Scarisbrick (Mayo) in myelin biology and Dr. Gomez Pinilla (UCLA) in central nervous system plasticity to investigate whether two highly targetable lifestyle variables, that is diet and exercise, can be modulated to improve myelin metabolism and functional recovery after SCI.
Institute:Mayo Clinic
Last Name:Scarisbrick
First Name:Isobel
Address:200 First St. SW, Rochester, Minnesota, 55905, USA
Email:scarisbrick.isobel@mayo.edu
Phone:507-284-0124

Subject:

Subject ID:SU000908
Subject Type:Mouse
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammal

Factors:

Subject type: Mouse; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Group
SA050207nC18-24oct16-018-r001PAR1-30d
SA050208nC18-24oct16-018-r002PAR1-30d
SA050209nC18-24oct16-020-r001PAR1-30d
SA050210nhilic-31oct16-018-r001PAR1-30d
SA050211pC18-19oct16-025-r001PAR1-30d
SA050212nhilic-31oct16-018-r002PAR1-30d
SA050213philic-28oct16-020-r001PAR1-30d
SA050214philic-28oct16-018-r002PAR1-30d
SA050215philic-28oct16-018-r001PAR1-30d
SA050216nC18-24oct16-020-r002PAR1-30d
SA050217nhilic-31oct16-025-r002PAR1-30d
SA050218nC18-24oct16-027-r001PAR1-30d
SA050219pC18-19oct16-027-r001PAR1-30d
SA050220nC18-24oct16-025-r001PAR1-30d
SA050221nC18-24oct16-025-r002PAR1-30d
SA050222nC18-24oct16-027-r002PAR1-30d
SA050223philic-28oct16-008-r002PAR1-30d
SA050224pC18-19oct16-027-r002PAR1-30d
SA050225nhilic-31oct16-025-r001PAR1-30d
SA050226philic-28oct16-008-r001PAR1-30d
SA050227pC18-19oct16-025-r002PAR1-30d
SA050228philic-28oct16-020-r002PAR1-30d
SA050229nC18-24oct16-008-r001PAR1-30d
SA050230nhilic-31oct16-008-r001PAR1-30d
SA050231nC18-24oct16-008-r002PAR1-30d
SA050232pC18-19oct16-018-r002PAR1-30d
SA050233philic-28oct16-025-r001PAR1-30d
SA050234philic-28oct16-025-r002PAR1-30d
SA050235nhilic-31oct16-027-r001PAR1-30d
SA050236nhilic-31oct16-027-r002PAR1-30d
SA050237pC18-19oct16-018-r001PAR1-30d
SA050238philic-28oct16-027-r001PAR1-30d
SA050239pC18-19oct16-008-r002PAR1-30d
SA050240pC18-19oct16-020-r001PAR1-30d
SA050241pC18-19oct16-020-r002PAR1-30d
SA050242nhilic-31oct16-008-r002PAR1-30d
SA050243nhilic-31oct16-020-r001PAR1-30d
SA050244nhilic-31oct16-020-r002PAR1-30d
SA050245pC18-19oct16-008-r001PAR1-30d
SA050246philic-28oct16-027-r002PAR1-30d
SA050247pC18-19oct16-012-r001PAR1-Control
SA050248nhilic-31oct16-021-r002PAR1-Control
SA050249pC18-19oct16-024-r002PAR1-Control
SA050250pC18-19oct16-022-r001PAR1-Control
SA050251pC18-19oct16-021-r002PAR1-Control
SA050252pC18-19oct16-022-r002PAR1-Control
SA050253pC18-19oct16-024-r001PAR1-Control
SA050254pC18-19oct16-021-r001PAR1-Control
SA050255nhilic-31oct16-021-r001PAR1-Control
SA050256nC18-24oct16-021-r001PAR1-Control
SA050257philic-28oct16-022-r001PAR1-Control
SA050258philic-28oct16-022-r002PAR1-Control
SA050259philic-28oct16-021-r002PAR1-Control
SA050260philic-28oct16-021-r001PAR1-Control
SA050261nC18-24oct16-012-r002PAR1-Control
SA050262nC18-24oct16-012-r001PAR1-Control
SA050263philic-28oct16-024-r001PAR1-Control
SA050264philic-28oct16-024-r002PAR1-Control
SA050265nhilic-31oct16-024-r001PAR1-Control
SA050266nhilic-31oct16-022-r002PAR1-Control
SA050267nhilic-31oct16-024-r002PAR1-Control
SA050268pC18-19oct16-014-r002PAR1-Control
SA050269nhilic-31oct16-012-r002PAR1-Control
SA050270nhilic-31oct16-012-r001PAR1-Control
SA050271nC18-24oct16-014-r001PAR1-Control
SA050272nC18-24oct16-014-r002PAR1-Control
SA050273nC18-24oct16-022-r001PAR1-Control
SA050274nC18-24oct16-021-r002PAR1-Control
SA050275nC18-24oct16-022-r002PAR1-Control
SA050276nhilic-31oct16-022-r001PAR1-Control
SA050277nC18-24oct16-024-r001PAR1-Control
SA050278pC18-19oct16-014-r001PAR1-Control
SA050279pC18-19oct16-012-r002PAR1-Control
SA050280philic-28oct16-012-r001PAR1-Control
SA050281nhilic-31oct16-014-r002PAR1-Control
SA050282nhilic-31oct16-014-r001PAR1-Control
SA050283philic-28oct16-014-r002PAR1-Control
SA050284philic-28oct16-014-r001PAR1-Control
SA050285philic-28oct16-012-r002PAR1-Control
SA050286nC18-24oct16-024-r002PAR1-Control
SA050287pC18-19oct16-029-r002PAR2-30d
SA050288nhilic-31oct16-006-r001PAR2-30d
SA050289nhilic-31oct16-006-r002PAR2-30d
SA050290nhilic-31oct16-004-r002PAR2-30d
SA050291nhilic-31oct16-004-r001PAR2-30d
SA050292pC18-19oct16-026-r002PAR2-30d
SA050293pC18-19oct16-029-r001PAR2-30d
SA050294pC18-19oct16-026-r001PAR2-30d
SA050295philic-28oct16-004-r001PAR2-30d
SA050296nC18-24oct16-026-r001PAR2-30d
SA050297nC18-24oct16-006-r002PAR2-30d
SA050298nC18-24oct16-026-r002PAR2-30d
SA050299nC18-24oct16-029-r001PAR2-30d
SA050300philic-28oct16-006-r002PAR2-30d
SA050301nhilic-31oct16-026-r001PAR2-30d
SA050302nC18-24oct16-006-r001PAR2-30d
SA050303philic-28oct16-026-r001PAR2-30d
SA050304philic-28oct16-029-r001PAR2-30d
SA050305philic-28oct16-029-r002PAR2-30d
SA050306nC18-24oct16-004-r001PAR2-30d
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Collection:

Collection ID:CO000902
Collection Summary:This prior project involved frozen whole mouse spinal cord (SC) samples for Untargeted Profiling (unbiased metabolomics assay). There were 9 samples total, n=3 for each genotype that includes wild type control, PAR1 KO and PAR2 KO at P60 days. Your team prepared the samples and ran the profiling and provided us with the results. Since the outcome of this preliminary study using 3 animals for each genotype looked so promising, we discussed bringing the total number to 5 and re-running to improve the power. Therefore, we are submitting 2 more samples for each genotype at P60. In addition, we are providing 5 samples for each genotype at P21 (an earlier age) for additional comparisons. To bring n=5 for each P60 genotype we provide 2 more samples per genotype. In addition we provide n=5 for P21 for each genotype (wild type, PAR1 and PAR2).
Sample Type:Spinal cord

Treatment:

Treatment ID:TR000922
Treatment Summary:A 3g Clip produces moderate SCI including demyelination and clinical impairment and we recently published a detailed methodology. At 1 week after injury, the 3g injured mice are expected to have an average Basso Mouse Scale score (BMS)=5 on a 9 point scale such that they have frequent plantar stepping with no or some coordination. This level of impairment was chosen to provide a sufficient window to observe recovery.

Sample Preparation:

Sampleprep ID:SP000915
Sampleprep Summary:large scale profiling of mouse spinal cord Lipids will be quantified in myelin isolated in high yield and purity by subcellular fractionation from the lumbosacral spinal cord. While there are no absolutely ‘myelin-specific’ lipids, galactocerebroside is the most typical of myelin in the adult nervous system being directly proportional to the amount of myelin. Sulfatide is another galactolipid enriched in myelin. Together with cholesterol, these form 78% of the total amount of lipid in the myelin membrane and each will be quantified using LC/MS/MS. A highly sensitive assay for galactocerebroside was recently established by the Mayo Metabolomics Core and can be implemented immediately. The LC/MS/MS panel for free fatty acids, including the very long chain fatty acids found in myelin is also routinely performed by the Core. Cholesterol will be quantified using an NMR-based approach by the Mayo Dept. of Laboratory Medicine Clinical Core. Additionally, we have a plan in place with the Metabolomics Core to develop LC/MS/MS assays for sulfatide and sphingomyelin during the Pilot proposal. Having quantitative assays for each of these key myelin lipids will facilitate our goal to comprehensively profile myelin lipid metabolism and will form foundational assays for a future NIH grant focused on myelin metabolism.

Combined analysis:

Analysis ID AN001418 AN001419 AN001420 AN001421
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity
Column Waters Acquity HSS C18 (150 x 2.1mm,1.8um) Waters Acquity HSS C18 (150 x 2.1mm,1.8um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI ESI
MS instrument type QTOF QTOF QTOF QTOF
MS instrument name Agilent 6550 QTOF Agilent 6550 QTOF Agilent 6550 QTOF Agilent 6550 QTOF
Ion Mode NEGATIVE POSITIVE NEGATIVE POSITIVE
Units intensity intensity intensity intensity

Chromatography:

Chromatography ID:CH000992
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity HSS C18 (150 x 2.1mm,1.8um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH000993
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Chromatography Type:HILIC

MS:

MS ID:MS001308
Analysis ID:AN001418
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS001309
Analysis ID:AN001419
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001310
Analysis ID:AN001420
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS001311
Analysis ID:AN001421
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
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